Malathion (MLT) is an organophosphorous type pesticide and having seriously high toxicity and electrochemical platforms for rapid, simple, inexpensive and sensitive determination of pesticides is still a special concern. This paper describes a simple preparation of a composite film consisting of ionic liquid (IL), chitosan (CS) and electrochemically synthesized gold nanoparticles (AuNPs) on single use pencil graphite electrodes (PGEs). The microscopic and electrochemical characterization of AuNP-CS-IL/PGE was studied using scanning electron microscopy, cyclic voltammetry and electrochemical impedance spectroscopy. This fabricated surface was then explored for the first time as a sensing matrix for the non-enzymatic electrochemical sensing of malathion by cyclic voltammetry and square wave voltammetry measurements. The proposed AuNP-CS-IL/PGE showed excellent characteristics and possessed remarkable affinity for malathion. The voltammetric current response exhibited two linear dynamic ranges, 0.89–5.94 nM and 5.94–44.6 nM reflecting two binding sites, with a detection limit of 0.68 nM. The method was applied in real sample analysis of apple and tomato. The results demonstrate the feasibility of AuNP-CS-IL-modified electrodes for simple, fast, ultrasensitive and inexpensive detection of MLT.